| 1. |
- Wang, Zhaoming, et al.
(author)
-
Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
-
In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
-
Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
|
|
| 2. |
- van der Post, Sjoerd, 1981, et al.
(author)
-
Site-specific O-glycosylation on the MUC2 mucin protein inhibits cleavage by the Porphyromonas gingivalis secreted cysteine protease (RgpB).
- 2013
-
In: The Journal of biological chemistry. - 1083-351X. ; 288:20, s. 14636-46
-
Journal article (peer-reviewed)abstract
- The colonic epithelial surface is protected by an inner mucus layer that the commensal microflora cannot penetrate. We previously demonstrated that Entamoeba histolytica secretes a protease capable of dissolving this layer that is required for parasite penetration. Here, we asked whether there are bacteria that can secrete similar proteases. We screened bacterial culture supernatants for such activity using recombinant fragments of the MUC2 mucin, the major structural component, and the only gel-forming mucin in the colonic mucus. MUC2 has two central heavily O-glycosylated mucin domains that are protease-resistant and has cysteine-rich N and C termini responsible for polymerization. Culture supernatants of Porphyromonas gingivalis, a bacterium that secretes proteases responsible for periodontitis, cleaved the MUC2 C-terminal region, whereas the N-terminal region was unaffected. The active enzyme was isolated and identified as Arg-gingipain B (RgpB). Two cleavage sites were localized to IR↓TT and NR↓QA. IR↓TT cleavage will disrupt the MUC2 polymers. Because this site has two potential O-glycosylation sites, we tested whether recombinant GalNAc-transferases (GalNAc-Ts) could glycosylate a synthetic peptide covering the IRTT sequence. Only GalNAc-T3 was able to glycosylate the second Thr in IRTT, rendering the sequence resistant to cleavage by RgpB. Furthermore, when GalNAc-T3 was expressed in CHO cells expressing the MUC2 C terminus, the second threonine was glycosylated, and the protein became resistant to RgpB cleavage. These findings suggest that bacteria can produce proteases capable of dissolving the inner protective mucus layer by specific cleavages in the MUC2 mucin and that this cleavage can be modulated by site-specific O-glycosylation.
|
|
| 3. |
- Ambort, Daniel, 1978, et al.
(author)
-
Calcium and pH-dependent packing and release of the gel-forming MUC2 mucin.
- 2012
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 109:15, s. 5645-50
-
Journal article (peer-reviewed)abstract
- MUC2, the major colonic mucin, forms large polymers by N-terminal trimerization and C-terminal dimerization. Although the assembly process for MUC2 is established, it is not known how MUC2 is packed in the regulated secretory granulae of the goblet cell. When the N-terminal VWD1-D2-D'D3 domains (MUC2-N) were expressed in a goblet-like cell line, the protein was stored together with full-length MUC2. By mimicking the pH and calcium conditions of the secretory pathway we analyzed purified MUC2-N by gel filtration, density gradient centrifugation, and transmission electron microscopy. At pH 7.4 the MUC2-N trimer eluted as a single peak by gel filtration. At pH 6.2 with Ca(2+) it formed large aggregates that did not enter the gel filtration column but were made visible after density gradient centrifugation. Electron microscopy studies revealed that the aggregates were composed of rings also observed in secretory granulae of colon tissue sections. The MUC2-N aggregates were dissolved by removing Ca(2+) and raising pH. After release from goblet cells, the unfolded full-length MUC2 formed stratified layers. These findings suggest a model for mucin packing in the granulae and the mechanism for mucin release, unfolding, and expansion.
|
|
| 4. |
- Johansson, Malin E V, 1971, et al.
(author)
-
Composition and functional role of the mucus layers in the intestine.
- 2011
-
In: Cellular and Molecular Life Sciences. - : Springer Science and Business Media LLC. - 1420-682X .- 1420-9071. ; 68, s. 3635-3641
-
Research review (peer-reviewed)abstract
- In discussions on intestinal protection, the protective capacity of mucus has not been very much considered. The progress in the last years in understanding the molecular nature of mucins, the main building blocks of mucus, has, however, changed this. The intestinal enterocytes have their apical surfaces covered by transmembrane mucins and the whole intestinal surface is further covered by mucus, built around the gel-forming mucin MUC2. The mucus of the small intestine has only one layer, whereas the large intestine has a two-layered mucus where the inner, attached layer has a protective function for the intestine, as it is impermeable to the luminal bacteria.
|
|
| 5. |
- Birchenough, George M. H., et al.
(author)
-
Altered Innate Defenses in the Neonatal Gastrointestinal Tract in Response to Colonization by Neuropathogenic Escherichia coli
- 2013
-
In: Infection and Immunity. - : American Society for Microbiology. - 0019-9567 .- 1098-5522. ; 81:9, s. 3264-3275
-
Journal article (peer-reviewed)abstract
- Two-day-old (P2), but not 9-day-old (P9), rat pups are susceptible to systemic infection following gastrointestinal colonization by Escherichia coli K1. Age dependency reflects the capacity of colonizing K1 to translocate from gastrointestinal (GI) tract to blood. A complex GI microbiota developed by P2, showed little variation over P2 to P9, and did not prevent stable K1 colonization. Substantial developmental expression was observed over P2 to P9, including upregulation of genes encoding components of the small intestinal (alpha-defensins Defa24 and Defa-rs1) and colonic (trefoil factor Tff2) mucus barrier. K1 colonization modulated expression of these peptides: developmental expression of Tff2 was dysregulated in P2 tissues and was accompanied by a decrease in mucin Muc2. Conversely, alpha-defensin genes were upregulated in P9 tissues. We propose that incomplete development of the mucus barrier during early neonatal life and the capacity of colonizing K1 to interfere with mucus barrier maturation provide opportunities for neuropathogen translocation into the bloodstream.
|
|
| 6. |
- Carvalho, F. A., et al.
(author)
-
Transient Inability to Manage Proteobacteria Promotes Chronic Gut Inflammation in TLR5-Deficient Mice
- 2012
-
In: Cell Host & Microbe. - : Elsevier BV. - 1931-3128. ; 12:2, s. 139-152
-
Journal article (peer-reviewed)abstract
- Colitis results from breakdown of homeostasis between intestinal microbiota and the mucosal immune system, with both environmental and genetic influencing factors. Flagellin receptor TLR5-deficient mice (T5KO) display elevated intestinal proinflammatory gene expression and colitis with incomplete penetrance, providing a genetically sensitized system to study the contribution of microbiota to driving colitis. Both colitic and noncolitic T5KO exhibited transiently unstable microbiotas, with lasting differences in colitic T5KO, while their noncolitic siblings stabilized their microbiotas to resemble wild-type mice. Transient high levels of proteobacteria, especially enterobacteria species including E. coli, observed in close proximity to the gut epithelium were a striking feature of colitic microbiota. A Crohn's disease-associated E. coli strain induced chronic colitis in T5KO, which persisted well after the exogenously introduced bacterial species had been eliminated. Thus, an innate immune deficiency can result in unstable gut microbiota associated with low-grade inflammation, and harboring proteobacteria can drive and/or instigate chronic colitis.
|
|
| 7. |
- Espinosa-Parrilla, Yolanda, et al.
(author)
-
Genetic association of gastric cancer with miRNA clusters including the cancer-related genes MIR29, MIR25, MIR93 and MIR106: Results from the EPIC-EURGAST study
- 2014
-
In: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 135:9, s. 2065-2076
-
Journal article (peer-reviewed)abstract
- MicroRNAs (miRNAs) are post-transcriptional gene regulators involved in a wide range of biological processes including tumorigenesis. Deregulation of miRNA pathways has been associated with cancer but the contribution of their genetic variability to this disorder is poorly known. We analyzed the genetic association of gastric cancer (GC) and its anatomical and histological subtypes, with 133 single-nucleotide polymorphisms (SNPs) tagging 15 isolated miRNAs and 24 miRNA clusters potentially involved in cancer, in 365 GC cases and 1,284 matched controls within the European Prospective Investigation into Cancer and Nutrition cohort. Various SNPs were associated with GC under the log-additive model. Furthermore, several of these miRNAs passed the gene-based permutation test when analyzed according to GC subtypes: three tagSNPs of the miR-29a/miR-29b-1 cluster were associated with diffuse subtype (minimum p-value=1.7 x 10(-4); odds ratio, OR=1.72; 95% confidence interval, CI=1.30-2.28), two tagSNPs of the miR-25/miR-93/miR-106b cluster were associated with cardia GC (minimum p-value=5.38 x 10(-3); OR=0.56, 95% CI=0.37-0.86) and one tagSNP of the miR-363/miR-92a-2/miR-19b-2/miR-20b/miR-18b/miR-106a cluster was associated with noncardia GC (minimum p-value=5.40 x 10(-3); OR=1.41, 95% CI=1.12-1.78). Some functionally validated target genes of these miRNAs are implicated in cancer-related processes such as methylation (DNMT3A, DNMT3B), cell cycle (E2F1, CDKN1A, CDKN1C), apoptosis (BCL2L11, MCL1), angiogenesis (VEGFA) and progression (PIK3R1, MYCN). Furthermore, we identified genetic interactions between variants tagging these miRNAs and variants in their validated target genes. Deregulation of the expression of these miRNAs in GC also supports our findings, altogether suggesting for the fist time that genetic variation in MIR29, MIR25, MIR93 and MIR106b may have a critical role in genetic susceptibility to GC and could contribute to the molecular mechanisms of gastric carcinogenesis.
|
|
| 8. |
- Ghorbanzadeh, Mehdi, et al.
(author)
-
In vitro and in silico derived relative effect potencies of Ah-Receptor-mediated effects by PCDD/Fs and PCBs in rat, mouse, and guinea pig CALUX Cell Lines
- 2014
-
In: Chemical Research in Toxicology. - : American Chemical Society (ACS). - 0893-228X .- 1520-5010. ; 27:7, s. 1120-1132
-
Journal article (peer-reviewed)abstract
- For a better understanding of species-specific relative effect potencies (REPs), responses of dioxin-like compounds (DLCs) were assessed. REPs were calculated using chemical-activated luciferase gene expression assays (CALUX) derived from guinea pig, rat, and mouse cell lines. Almost all 20 congeners tested in the rodent cell lines were partial agonists and less efficacious than 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). For this reason, REPs were calculated for each congener using concentrations at which 20% of the maximal TCDD response was reached,(REP20TCDD). REP20TCDD values obtained for PCDD/Fs were comparable with their toxic equivalency factors assigned by the World Health Organization (WHO-TEF), while those for PCBs were in general lower than the WHO-TEF values. Moreover, the guinea pig cell line was the most sensitive as indicated by the 20% effect concentrations of TCDD of 1.5, 5.6, and 11.0 pM for guinea pig, rat, and mouse cells, respectively. A similar response pattern was observed using multivariate statistical analysis between the three CALLTX assays and the WHO-TEFs. The mouse assay showed minor deviation due to higher relative induction potential for 2,3,7,8-tetrachlorodibenzofuran and 2,3,4,6,7,8-hexachlorodibenzofuran and lower for 1,2,3,4,6,7,8-heptachlorodibenzofuran and 3,3',4,4',5-pentachlorobiphenyl (PCB126). 2,3,7,8-Tetrachlorodibenzofuran was more than two times more potent in the mouse assay as compared with that of rat and guinea pig cells, while measured REP20TCDD for PCB126 was lower in mouse cells (0.05) as compared with that of the guinea pig (0.2) and rat (0.07). In order to provide REP20TCDD values for all WHO-TEF assigned compounds, quantitative structure activity relationship (QSAR) models were developed. The QSAR models showed that specific electronic properties and molecular surface characteristics play important roles in the AhR-mediated response. In silica derived REP20TCDD values were generally consistent with the WHO-TEFs with a few exceptions. The QSAR models indicated that, e.g., 1,2,3,7,8-pentachlorodibenzofuran and 1,2,3,7,8,9-hexachlorodibenzofuran were more potent than given by their assigned WHO-TEF values, and the non-ortho PCB 81 was predicted, based on the guinea-pig model, to be 1 order of magnitude above its WHO-TEF value. By combining in vitro and in silico approaches, REPs were established for all WHO-TEF assigned compounds (except OCDD), which will provide future guidance in testing AhR-mediated responses of DLCs and to increase our understanding of species variation in AhR-mediated effects.
|
|
| 9. |
- Johansson, Malin B., et al.
(author)
-
Electronic and optical properties of nanocrystalline WO3 thin films studied by optical spectroscopy and density functional calculations
- 2013
-
In: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 25:20, s. 205502-
-
Journal article (peer-reviewed)abstract
- The optical and electronic properties of nanocrystalline WO3 thin films prepared by reactive dc magnetron sputtering at different total pressures (P-tot) were studied by optical spectroscopy and density functional theory (DFT) calculations. Monoclinic films prepared at low P-tot show absorption in the near infrared due to polarons, which is attributed to a strained film structure. Analysis of the optical data yields band-gap energies E-g approximate to 3.1 eV, which increase with increasing P-tot by 0.1 eV, and correlate with the structural modifications of the films. The electronic structures of triclinic delta-WO3, and monoclinic gamma- and epsilon-WO3 were calculated using the Green function with screened Coulomb interaction (GW approach), and the local density approximation. The delta-WO3 and gamma-WO3 phases are found to have very similar electronic properties, with weak dispersion of the valence and conduction bands, consistent with a direct band-gap. Analysis of the joint density of states shows that the optical absorption around the band edge is composed of contributions from forbidden transitions (>3 eV) and allowed transitions (>3.8 eV). The calculations show that E-g in epsilon-WO3 is higher than in the delta-WO3 and gamma-WO3 phases, which provides an explanation for the P-tot dependence of the optical data.
|
|
| 10. |
- Johansson, Malin B., et al.
(author)
-
Optical properties of nanocrystalline WO3 and WO3-x thin films prepared by DC magnetron sputtering
- 2014
-
In: Journal of Applied Physics. - : American Institute of Physics (AIP). - 0021-8979 .- 1089-7550. ; 115:21, s. 213510-
-
Journal article (peer-reviewed)abstract
- The optical properties of tungsten trioxide thin films prepared by DC magnetron sputtering, withdifferent oxygen vacancy (Vo) concentration, have been studied by spectrophotometry andphotoluminescence (PL) emission spectroscopy. Absorption and PL spectra show that the filmsexhibit similar band gap energies, Eg 2.9 eV. The absorption spectra of the films show twopronounced absorption bands in the near-infrared region. One peak (P1) is located atapproximately 0.7 eV, independent of Vo concentration. A second peak (P2) shifts from 0.96 eV to1.16 eV with decreasing Vo concentration. Peak P1 is assigned to polaron absorption due totransitions between tungsten sites (W5þ!W6þ), or an optical transition from a neutral vacancystate to the conduction band, Vo0!W6þ. The origin of peak P2 is more uncertain but may involveþ1 and þ2 charged vacancy sites. The PL spectra show several emission bands in the range 2.07 to3.10 eV in the more sub-stoichiometric and 2.40 to 3.02 eV in the less sub-stoichiometric films.The low energy emission bands agree well with calculated optical transition energies of oxygenvacancy sites, with dominant contribution from neutral and singly charged vacancies in the lesssub-stoichiometric films, and additional contributions from doubly charged vacancy sites in themore sub-stoichiometric films.
|
|
| 11. |
- Johansson, Malin B, et al.
(author)
-
Structural and optical properties of visible active photocatalytic WO3 thin films prepared by reactive dc magnetron sputtering
- 2012
-
In: Journal of Materials Research. - : Springer Science and Business Media LLC. - 0884-2914 .- 2044-5326. ; 27:24, s. 3130-3140
-
Journal article (peer-reviewed)abstract
- Nanostructured tungsten trioxide films were prepared by reactive dc magnetron sputteringat different working pressures P-tot = 1-4 Pa. The films were characterized by scanning electron microscopy, x-ray diffraction, Rutherford backscattering spectroscopy, Raman spectroscopy, and ultraviolet-visible spectrophotometry. The films were found to exhibit predominantly monoclinic structures and have similar band gap, E-g approximate to 2.8 eV, with a pronounced Urbach tail extending down to 2.5 eV. At low P-tot, strained film structures formed, which were slightly reduced and showed polaron absorption in the near-infrared region. The photodegradation rate of stearic acid was found to correlate with the stoichiometry and polaron absorption. This is explained by a recombination mechanism, whereby photoexcited electron-hole pairs recombine with polaron states in the band gap. The quantum yield decreased by 50% for photon energies close to E-g due to photoexcitations to band gap states lying below the O-2 affinity level.
|
|
| 12. |
- Sellstedt, Magnus, 1981-, et al.
(author)
-
Synthesis and Characterization of a Multi Ring-Fused 2-Pyridone-Based Fluorescent Scaffold
- 2010
-
In: European Journal of Organic Chemistry. - : Wiley. - 1434-193X .- 1099-0690. ; :32, s. 6171-6178
-
Journal article (peer-reviewed)abstract
- A series of compounds based on a novel fluorescent scaffold have been synthesized. Most of the compounds displayed high quantum yields of fluorescence and unusually long fluorescence lifetimes. HeLa cells were treated with one of the compounds and its use as a fluorescent dye was demonstrated with fluorescence confocal microscopy.
|
|
| 13. |
- Subramani, Durai B, et al.
(author)
-
Lactobacillus and Bifidobacterium species do not secrete protease that cleaves the MUC2 mucin which organises the colon mucus.
- 2010
-
In: Beneficial microbes. - 1876-2891. ; 1:4, s. 343-50
-
Journal article (peer-reviewed)abstract
- The colon epithelium is covered by two layers of mucus built around the MUC2 mucin. An inner dense and attached mucus layer does not allow bacteria to penetrate, thus keeping the epithelial cell surface free from bacteria. An outer loose mucus layer is the habitat for the commensal bacterial microbiota. The inner mucus layer is renewed from the epithelial side and gets converted into the outer layer due to proteolytic cleavages by host proteases. We have now analysed if potential probiotic bacteria, namely Lactobacillus brevis, Lactobacillus plantarum, Lactobacillus bulgaricus and Bifidobacterium lactis, can secrete protease that cleaves the MUC2 mucin. We found that none of the potential probiotic bacteria Lactobacillus and Bifidobacterium could cleave the MUC2 core protein in the form of recombinant MUC2 N and C-termini although they secreted active proteases. This was in contrast to crude mixtures of oral and faecal bacteria that cleaved the MUC2 mucin. This observation further supports the view that these potential probiotic bacteria are of no harm to the host, as these bacteria cannot disrupt the mucin organised mucus as long as they are covered by glycans.
|
|
